crobb305 - 4:15 am on May 10, 2012 (gmt 0)
It's interesting that you think keyword stuffing is your problem. Most of the comments I read had more to do with gaming of links.
I think it's largely an on-site issue as well. Document-level classifiers such as N-grams can reveal excessive use of known phrases. I believe these can occur in body text or in anchor text (on page). For instance, linking to the same internal page 5 times on the homepage with varying anchor text or using redundant language (including synonyms), or covering too many known phrases for your site's theme. It's interesting to me that the only item in Google's list of 52 search-quality changes from April that has anything to do with spam is "keyword stuffing". That may be a hint.